Looking to install my Seaway replacment windows which come with a sill adapter that snaps into a channel in the bottom of the window (it is flat and just terminates where it hits the existing sill-it is not in an L shape like others i have seen).

Ive seen it done two ways , install the sill adapter before installing window and then putting a strip of low expansion foam on the sill right before install. Or install the window without the adapter, insulate underneath, then install sill adapter. With the second way i am concerned because i would have to cut the adapter to fit in between the exterior stops (i am doing inside install) and it will not extend the full length of the actual window opening. Is there a best way to do it?

On another note, because of the interior install (and getting over the stool) i sized the windows a little less than 1/2 under the rough opening on height. Is there a problem with shimming the sill up an 1/8-1/4in with plywood so the top hits the exterior stop without using a head expander?

I also saw a few installs where people recommend putting flashing tape on the sill, and extending it 6 inches up each jamb. Is this common practice and should i do it?

I've never done it before, always after. Yes, you can shim upwards to desired height not to exceed the gap that the adapter will cover regarding the sill pitch. You just need to shim the inside sill corners that meet the stool and not a continuous piece of wood across the entire length of the replacement window's sill.

If you are concerned about the sill angle adapter not being behind the stops you could leave the bottom exterior face ever so slightly off the interior face of the exterior stop. Then cut the length of the sill angle to exceed the inner dimension between the two stops. Start at one corner and fish it in behind the stop and push it in with kind of a mutant terminator thumb push with your hands, or slightly tap in utilizing a small block of wood or PVC to achieve the "snap" fully seated position. I'd work both corners in first then take the bow out of the face in the middle. Don't cut too wide as the sill angle will jamb up in the weld flash in the corners of the face accessory groove.

Be careful not to overfill the center sill area with too much low-expansion foam as that can frown or crown up the vinyl sill slightly. Even with the best of foams this is a common issue we have to deal with. We fill the corners completely even trying to get some up the side jambs. I only do one nice sized interior pass that is pretty deep towards the stool.

Always after! You can shim it up with shims to get it in place. We do the entire install saving the sill expander so for last. We do it while cleaning up. We foam under the sill during the install to make sure it's sealed tightly. Then we cut the expander to the proper height and pound it in place. The expander is wider and tucks nicely behind the blind stops into the groove. I use a vinyl block that's 8" X 3" X 1/2" to set it in place. Just tap in one side behind the stop and continue to pound it in the groove. Half way down you want to start the other side so it tucks in behind the stop. Once it all gets popped in the groove it flattens out nicely. It will make more sense after you do one. If it's cold out make sure you keep them warm. Otherwise they will split down the middle. Good Luck!!!